Getting Started
The FLUX CAPACITOR is run with the command
./flux capacitor -ref <file.gtf> -bed <file.bed> [-out <file.gtf>] [-f]
Supported parameters:
| short | | explanation |
| -ref <file.gtf> | | specifies the location of the GTF file containing the reference genome. This parameter is mandatory and the program will exit in case no or an invalid file is provided here. For a specification of the supported GTF format, refer to File Formats or have a look at the downloadable example file. |
-bed <file.bed> | | specifies the path of the BED file with the sequencer reads. Also this parameter is mandatory, see File Formats or the example for a description of the respective formatting. |
-out <file.gtf> | | An optional parameter to provide the location of a file for the GTF output. If none is specified, the program will write to stdout and can be redirected by the default platform supported stream piping. |
| -f | | F for force. Suppresses any output of the program -- usually FLUX is quite talkative on stderr. The parameter enables the embedding of the program into |
As by version 1.0, the FLUX CAPACITOR exclusively interprets single reads from the input BED file, and exclusively permits one read length (as interpreted by the first line of input). Intermediate versions already overcome these limitations and will be included in one of the next released packages. If you are interested, contact me at MICHA at SAMMETH dot NET, and I will
